Variant report

Variant	rs2017448
Chromosome Location	chr16:69719724-69719725
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:69718628..69722517-chr16:69722736..69727715,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102908	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11075729	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11640319	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12918548	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12933210	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1437134	0.83[AFR][1000 genomes]
rs1469908	0.83[AFR][1000 genomes]
rs1837016	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2161630	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2917670	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2917671	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3848278	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs45488899	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4633710	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55780735	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6499241	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7187634	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7189878	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7191292	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7192380	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7192543	0.86[EUR][1000 genomes]
rs7205551	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7359336	0.81[AFR][1000 genomes]
rs8045432	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8049728	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8055756	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8061052	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9938213	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906822	chr16:69711533-69745145	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2017448	LOC440348	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69667000-69727600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:69671200-69726400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr16:69681600-69725800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:69681600-69725800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr16:69685000-69724800	Weak transcription	Fetal Heart	heart
6	chr16:69688600-69725400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr16:69690200-69725800	Weak transcription	Ovary	ovary
8	chr16:69691000-69726400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr16:69694800-69725800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr16:69700400-69725400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr16:69701400-69725600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr16:69701800-69739200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr16:69704000-69725400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr16:69704600-69737800	Strong transcription	Liver	Liver
15	chr16:69705800-69725800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr16:69705800-69725800	Weak transcription	Gastric	stomach
17	chr16:69705800-69725800	Weak transcription	Small Intestine	intestine
18	chr16:69705800-69726000	Weak transcription	Psoas Muscle	Psoas
19	chr16:69706000-69725000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr16:69706000-69726200	Weak transcription	Stomach Mucosa	stomach
21	chr16:69706200-69725800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr16:69706200-69725800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr16:69706200-69725800	Weak transcription	Right Ventricle	heart
24	chr16:69706400-69725800	Weak transcription	Brain Angular Gyrus	brain
25	chr16:69708800-69739600	Strong transcription	Placenta	Placenta
26	chr16:69709000-69739400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr16:69709200-69720600	Strong transcription	Primary T cells from cord blood	blood
28	chr16:69709400-69720400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr16:69709400-69721600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr16:69709400-69755400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr16:69709600-69720800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr16:69709600-69721200	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr16:69709600-69723600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr16:69709600-69724600	Strong transcription	Fetal Intestine Large	intestine
35	chr16:69709600-69726800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr16:69709800-69721600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr16:69709800-69737000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr16:69710000-69721600	Strong transcription	Fetal Lung	lung
39	chr16:69710000-69737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr16:69710200-69719800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr16:69710800-69732000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr16:69711600-69723800	Strong transcription	Fetal Stomach	stomach
43	chr16:69711600-69723800	Weak transcription	K562	blood
44	chr16:69711600-69725600	Weak transcription	Fetal Brain Male	brain
45	chr16:69711800-69723000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr16:69711800-69723800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr16:69711800-69723800	Strong transcription	Fetal Intestine Small	intestine
48	chr16:69712800-69723800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr16:69712800-69725800	Weak transcription	Brain Germinal Matrix	brain
50	chr16:69712800-69725800	Weak transcription	Brain Substantia Nigra	brain

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